The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism.
The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism.
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RNA-seq 和 microRNA-seq 的综合分析描绘了与日本牙鲆 (Paralichthys olivaceus) 白化病有关的 miRNA-mRNA 网络
DOI：
10.1371/journal.pone.0181761
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Chen S
中科院分区：
文献类型：
--
作者：
Wang N;Wang R;Wang R;Tian Y;Shao C;Jia X;Chen S
白化病是一种以日本比目鱼（Paralichthys olivaceus）眼侧色素缺乏为特征的现象，已造成严重损害。有限的mRNA和microRNA（miRNA）的信息可用于鱼类色素缺乏症。本研究采用高通量测序技术对影响褐飞虱白化的mRNA和miRNAs进行了鉴定。RNA-seq以牙鲆基因组为基础，通过转录本组装鉴定出21,787个已知基因和711个新基因。其中，235个基因表现出显著不同的表达模式（倍数变化≥2或≤0.5，q值≤0.05），包括194个下调基因和41个上调基因在白化病与正常色素个体。这些基因富集到81个GO术语和9个KEGG途径（p≤0.05）。其中包括色素沉着的相关途径-黑素生成和酪氨酸代谢。高通量miRNA测序共鉴定出475个miRNA，包括64个新的miRNA。此外，在白化病与正常色素个体中鉴定了33种差异表达的miRNA，其中包括13种上调和20种下调的miRNA（倍数变化≥1.5或≤0.67，p≤0.05）。进一步的靶基因预测发现了多种可能的靶基因，其中酪氨酸酶（Tyrosinase，TYR）、酪氨酸酶相关蛋白1（Tyrosinase-related protein 1，TYRP 1）、小眼症相关转录因子（Microphthalmia-associated transcription factor，MITF）等134个基因与RNA-seq的差异表达基因重叠。这些靶基因显著富集到254个GO术语和103个KEGG途径（p<0.001）。其中，酪氨酸代谢、溶酶体、光转导途径等，由于它们参与调节皮肤色素沉着而引起相当大的关注。通过qRT-PCR在10种mRNA和10种miRNA中验证差异表达的mRNA和miRNA的表达模式。通过高通量的mRNA和miRNA测序和分析，鉴定了一系列与鱼类色素沉着有关的mRNA和miRNA。miRNA-mRNA调控网络也为进一步阐明鱼类色素缺乏症提供了坚实的起点。
Albinism, a phenomenon characterized by pigmentation deficiency on the ocular side of Japanese flounder (Paralichthys olivaceus), has caused significant damage. Limited mRNA and microRNA (miRNA) information is available on fish pigmentation deficiency. In this study, a high-throughput sequencing strategy was employed to identify the mRNA and miRNAs involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05). The next target prediction discovered a variety of putative target genes, of which, 134 genes including Tyrosinase (TYR), Tyrosinase-related protein 1 (TYRP1), Microphthalmia-associated transcription factor (MITF) were overlapped with differentially expressed genes derived from RNA-seq. These target genes were significantly enriched to 254 GO terms and 103 KEGG pathways (p<0.001). Of those, tyrosine metabolism, lysosomes, phototransduction pathways, etc., attracted considerable attention due to their involvement in regulating skin pigmentation. Expression patterns of differentially expressed mRNA and miRNAs were validated in 10 mRNA and 10 miRNAs by qRT-PCR. With high-throughput mRNA and miRNA sequencing and analysis, a series of interested mRNA and miRNAs involved in fish pigmentation are identified. And the miRNA-mRNA regulatory network also provides a solid starting point for further elucidation of fish pigmentation deficiency.
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